Wednesday 19 December 2012 13.11 EST
First published on Wednesday 19 December 2012 13.11 EST

A scandal that threatened to derail a crucial transition of leadership at the New York Times Company appears to be heading toward resolution with the reputation of the paper's new president and chief executive intact.

Mark Thompson joined the Times Company in November after eight years as director general of the BBC. An independent report, published on Wednesday, into potential misconduct at the corporation during Thompson's tenure found evidence of "chaos and confusion" and a failure of leadership – but no egregious ethical lapse.

The report concluded there was "no reason to doubt" Thompson's testimony that he had not focused on the internal controversy in part because he missed other media stories about it.

The independent review, headed by former Sky News chief Nick Pollard, examined whether the BBC had suppressed a report on alleged criminal sexual misconduct by longtime BBC presenter Jimmy Savile. Pollard's review found that the Savile story had been shelved for editorial concerns that Pollard found to be misguided.

Thompson said he first heard about the story, produced by the BBC's Newsnight programme, at a 2011 Christmas party. He then asked a deputy about it, "received reassurance, and indeed got the sense the whole matter was closed, crossed it off my list and went off to worry about something else," he told Pollard.

"Mr Thompson checked the story out with BBC News but learned no specifics of the investigation," Pollard concluded. "Indeed, Mr Thompson told me that the various press stories which followed passed him by. I have no reason to doubt what he told me."

Lord Patten, the chairman of the BBC Trust, was challenged about Thompson's role at a press conference launching the report on Wednesday. Frustrated by the pointed questioning, he said: "I have no reason at all to disbelieve Mark Thomson. Is that an answer?"

Thompson was announced as the incoming head of the Times company in August. As the BBC scandal grew in the autumn, the New York Times reported aggressively on Thompson's potential role.

The paper's coverage, led by investigative reporter Matthew Purdy, included assessments of Thompson's conduct that are more scathing than anything in the Pollard review.

A November dispatch headlined "As scandal flared, BBC's leaders missed red flags" said Thompson and others "repeatedly missed opportunities to pursue a fuller picture" of what had happened. An October Times story quoted former BBC producer Roger Gale as saying that Thompson was well paid "to, apparently, not know what was going on under his own roof."

The chief executive job at the Times Company sat vacant for almost a year after Janet Robinson, who began in 2004, resigned in December 2011. During her tenure the share price fell from the mid-30s to less than $8, the paper reported.